Variant report

Variant	rs1877604
Chromosome Location	chr1:94136064-94136065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94134360..94137272-chr1:94311581..94314212,2	MCF-7	breast:
2	chr1:94117141..94121029-chr1:94132853..94136106,3	K562	blood:
3	chr1:94109497..94111202-chr1:94135455..94137593,2	MCF-7	breast:
4	chr1:94125982..94128788-chr1:94135746..94137501,2	K562	blood:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	1.00[ASN][1000 genomes]
rs11579004	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11579685	1.00[ASN][1000 genomes]
rs11580965	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588860	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12066343	1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs12732557	1.00[ASN][1000 genomes]
rs12739747	1.00[ASN][1000 genomes]
rs12740779	1.00[ASN][1000 genomes]
rs12744941	1.00[ASN][1000 genomes]
rs12757325	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12760092	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17110063	1.00[ASN][1000 genomes]
rs17110101	1.00[ASN][1000 genomes]
rs17110111	1.00[ASN][1000 genomes]
rs17110179	0.85[AMR][1000 genomes]
rs17110225	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877605	1.00[CHB][hapmap]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423897	1.00[ASN][1000 genomes]
rs34663884	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34666525	1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	1.00[ASN][1000 genomes]
rs35972761	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36115605	1.00[ASN][1000 genomes]
rs3950119	1.00[ASN][1000 genomes]
rs59996315	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61780979	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61780999	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6683296	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66966060	1.00[ASN][1000 genomes]
rs67043929	1.00[ASN][1000 genomes]
rs67300695	1.00[ASN][1000 genomes]
rs67354439	1.00[ASN][1000 genomes]
rs67511232	1.00[ASN][1000 genomes]
rs71652539	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72721041	1.00[ASN][1000 genomes]
rs7511890	1.00[ASN][1000 genomes]
rs7525880	1.00[ASN][1000 genomes]
rs7531106	1.00[ASN][1000 genomes]
rs7543098	1.00[ASN][1000 genomes]
rs7543763	1.00[ASN][1000 genomes]
rs7553185	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7555302	1.00[ASN][1000 genomes]
rs761802	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1877604	SNORD21	cis	cerebellum	SCAN
rs1877604	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94127400-94143800	Genic enhancers	HMEC	breast
2	chr1:94127400-94144000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:94128800-94137800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:94129000-94137000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:94129200-94144800	Weak transcription	GM12878-XiMat	blood
6	chr1:94129400-94137600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:94130800-94141000	Genic enhancers	HSMM	muscle
8	chr1:94131000-94138000	Weak transcription	Fetal Brain Male	brain
9	chr1:94131200-94136200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:94131200-94136200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:94131200-94144000	Genic enhancers	Placenta	Placenta
12	chr1:94131400-94136400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:94131400-94137000	Genic enhancers	A549	lung
14	chr1:94131400-94140600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:94131600-94136200	Weak transcription	Fetal Lung	lung
16	chr1:94131600-94143800	Genic enhancers	NHEK	skin
17	chr1:94131800-94140400	Genic enhancers	NHDF-Ad	bronchial
18	chr1:94132400-94139600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:94132800-94137000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:94132800-94137800	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr1:94132800-94137800	Weak transcription	Pancreas	Pancrea
22	chr1:94132800-94138000	Weak transcription	Fetal Kidney	kidney
23	chr1:94132800-94138600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:94132800-94141000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:94132800-94141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:94132800-94141800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:94132800-94142400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:94132800-94142600	Enhancers	Adipose Nuclei	Adipose
29	chr1:94132800-94144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:94133000-94136400	Enhancers	Stomach Mucosa	stomach
31	chr1:94133000-94137800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:94133000-94137800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:94133000-94141600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:94133000-94142000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:94133400-94136800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:94133400-94137800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:94133400-94138000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:94133400-94141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:94134000-94136400	Enhancers	HSMMtube	muscle
40	chr1:94134000-94136800	Enhancers	Fetal Muscle Leg	muscle
41	chr1:94134000-94137000	Weak transcription	Esophagus	oesophagus
42	chr1:94134000-94137600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:94134000-94137600	Genic enhancers	Hela-S3	cervix
44	chr1:94134000-94137800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:94134000-94138000	Weak transcription	Psoas Muscle	Psoas
46	chr1:94134200-94136200	Weak transcription	HepG2	liver
47	chr1:94134200-94136200	Enhancers	NHLF	lung
48	chr1:94134400-94140800	Genic enhancers	Osteobl	bone
49	chr1:94134600-94136200	Strong transcription	Primary B cells from cord blood	blood
50	chr1:94134600-94136200	Enhancers	Brain Angular Gyrus	brain

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